Setting up a IAX Trunk is very similar to a SIP Trunk, the biggest difference in registration is the Register String. The IAX trunk contains more information than a SIP Trunk. Trunk information can be copied over just like setting up the SIP Trunks
Make sure to set the registration string as; username:password@domain
If you would like to see if trunks are registered you can go to the FreePBX System Status and look at IP Trunk Registrations.
In the SIP Trunk make sure the contact field behind the registration string. The setup for the registration string will be username:password@domain/sipContact(username)
After you have created your IAX Trunk you need to modify the Asterisk IAX Settings inside the Tools.
Inside here you will be able to make changes to the Codec's, bandwidth control, and multiple other settings.
These items will need to be checked if you have any special type of NAT setup inside the firewall or company.
Be sure to open up Port 4569 inside your firewall, as well as ports 10,000-20,000 which are mainly for SIP, but IAX uses some of those ports